refactor(config): config/state mutators flush, callers commit (E3 S3, B-core-10)

Restores CLAUDE.md's canonical transaction rule ("the handler commits; helpers
flush; only quota owns its session") on the config path: sysconfig.set_value /
sysconfig.reset and state.set_sync_paused now flush instead of committing, so a
change lands in ONE transaction with the audit row the route records for it —
previously the helper's internal commit split them, and a crash between left the
mutation persisted with no audit trail.

All callers already commit (the config PATCH/DELETE + audit, the sync pause/resume
+ audit, the scheduler maintenance PATCH); the setup wizard, which relied on the
internal commit, gets an explicit db.commit() after its loop. apply_interval is
deliberately left committing — it performs a live APScheduler reschedule that must
follow the DB persist, so it owns its own unit of work (a legitimate exception,
like the download service transitions). New test locks the flush-not-commit
contract (a rollback before the caller commits discards the change). 368 pass.

backend/app/routes/setup.py

@@ -96,6 +96,7 @@ def setup_config(settings_map: dict[str, Any], db: Session = Depends(require_set
         except (ValueError, RuntimeError) as exc:
             raise HTTPException(status_code=400, detail=str(exc))
         saved.append(key)
+    db.commit()  # sysconfig.set_value only flushes now — persist the wizard's config in one commit
     return {"saved": saved}